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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattggtcactatttccttcctgtgttgttgttgtttattttttttgctagaactgtcatggtctcatagatcagatgttattgaatcgttttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTGTGGCTTGCCTATTAGCACATACTTCAGTGCTTTGAAGCTGCTGTGGTTG

Basic information

species Glycine max
transcript GLYMA07G03230.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03230.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ13112 (Selaginella moellendorffii), 3'ss of exon 2
-------aattggtcactatttccttcctgtgttgttgttgtttattttttttgctagaactgtcatggtctcatagatcagatgttattgaatcgttttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTGTGGCTTGCCTATTAGCACATACTTCAGTGCTTTGAAGCTGCTGTGGTTG
       |  | |          | |   || ||  | || | | | |  |||| | |   |||| || | |  |      ||| || ||   |  |||     |||  | |||||| || |  | || || || || || || |||||||| || |||||  | || || ||||| |||||||||||||||||||| |||||| ||
cctccatagctcgatctggaaagcctaaagtatttcttttttctttctcgtttgtttgttttgtcgtgttttagt------gat-ttcttatcttctttcttggcagACGCTTGGAAGAGAATCTCTCCGGTGGAAGCAAACACTTTGTGGAAAGCTGTGGACTTCCCATAAGCACTTACTTCAGTGCTTTGAAGCTACTGTGGCTG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|213600377|gb|DB966170.1|DB966170
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|213615123|gb|DB962835.1|DB962835
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|192299331|gb|FG992509.1|FG992509
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GATATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|298190364|gb|HO032485.1|HO032485
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTCGCAG                         GAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|192328693|gb|FK023179.1|FK023179
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GAGATTGGGAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|209697480|gb|BW669981.1|BW669981
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|308098155|gb|HO761326.1|HO761326
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
EST: gi|192331610|gb|FK019971.1|FK019971
EST:     CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAG                         GAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG
genomic: CTTCACAACGCCATTGTTTGGATGGATGCTCGCACTTCTTCCATTTGCAGgtcaactatt ... tttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctagaactgtcatggtctcatagatcagatgttattgaatcgttttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTGTGGCTTGCCTATTAGCACATACTTCAGTGCTTTGAAGCTGCTGTGGTTG
                                         tcgtttt  CT-rich tract
                                 ttattgaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattggtcactatttccttcctgtgttgttgttgtttattttttttgctagaactgtcatggtctcatagatcagatgttattgaatcgttttgaaacagGAGATTGGAAAAGGAGTTATCTGGCGGTAGAAACCATTTTGTGGAGAGTTGTGGCTTGCCTATTAGCACATACTTCAGTGCTTTGAAGCTGCTGTGGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - -ccttcct
- - - - - - - - - - - - gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -catggtc